He realised they were above profile and made the captain aware of this fact twice, but having been commander on other aircraft types before he did not want to encroach the captain's decisions.....Following the flight he believed he confused sympathy and cockpit resource management, which prevented him to fulfill his role as pilot monitoring.
This extreme politeness and unwillingness to challenge another crew-member seems to me to be similar to what we know of AF447. What's the cockpit culture in AF?